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In the Beginning is the second of six Babylon 5 TV movies. It is set primarily in December 2278 on Londo Mollari’s final day alive, looking back on events preceding, during, and shortly after the Earth-Minbari War.

The story of the Earth-Minbari War is told from the memories of G'Kar, Delenn and Londo Mollari. Delenn declares there is normally one singular moment that defines a generation. G'Kar describes war as the history of pain, however, with its end hopefully grows a more mature nature that gives hope for the future. Delenn agrees, as out of the War came Babylon 5.

Two children, Luc and Lyssa, are playing and find themselves in the Emperor's chamber, which has the only non-barred window in the palace. Senna Refa finds them, and tries to hurry them out of the chamber where they are not allowed to be. Mollari is there, but he is pleased to see the children. He gives Luc his Seal and allows him to give one order as Emperor. He asks for a grand story, and Lyssa timidly adds that it has to be true. Mollari grants both wishes.

His story starts with the Humans, who occupied an uninteresting part of the galaxy, but the Centauri, being a decadent culture, were intrigued by their art and eccentricity. Mollari notes that the Humans' pride would be their undoing.

In 2243, Mollari was a liaison to Earth's Centauri delegation. He was called to meet General Robert Lefcourt and Hastur, aide to the President. The General explains Earth's recent advancement of their sphere of influence following their successful part in the Dilgar War. They want to learn about all cultures, but some are still a mystery, including the Minbari. Mollari does not admit much information. Rather, he recommends they stay away from them, as even the Centauri refused to challenge them. The two Humans laugh at this, and dismiss any implication that they cannot take care of themselves. Mollari calls it arrogance and stupidity, and leaves, but not without promising locations of military installations so they can at least avoid them.

On Minbar, Callier is met by Anla'ShokLenonn, who earlier requested more support from the Council of Caste Elders. Callier informs him it was rejected, as they feel they have already fulfilled their promise to Valen and belief in the coming Shadow War is fading. Lenonn wants to take his request to the Grey Council, but Callier recommends against it, as it might risk adverse action. Lenonn is not concerned, as everyone will pay the price if he is not heard.

Later in the night, Lenonn finds six aides in his room who lead him silently to a spot where they are taken to the Cruiser of the Council. Dukhat calls him to the center of the Council's chamber.

Luc interrupts Mollari's story, wondering when the battle will start. Mollari insists this leads to the War, and a terrible truth: the blood of those who died is on his hands.

Refa humbly says Mollari cannot hold himself accountable, but Mollari says he knows what he did.

Lenonn recounts Valen's prophecy and says the time is almost there. He is tired of being marginalized by even some on the Council. Dukhat notes that the prophecy also stated that the Rangers will arise so why not wait for that before asking the worker and warrior castes to commit resources. Indeed, Lenonn can only say he believes, but also that they should meet the Vorlons. Coplann takes off his hood and chimes in – a dozen ships have tried and been lost. Since they know the prophecy as well, why not wait for something to believe in. At this point, Delenn unhoods and suggests this proof could be obtained by going to Z'ha'dum to see if the Shadows have returned. Coplann objects to risking more warriors on the journey, and Dukhat agrees – he decides they themselves will make the trip.

As Dukhat and Delenn leave the chamber, she notes both Lenonn and Coplann are right. Dukhat understands, and leaves to meditate. In his chamber, Kosh appears. Dukhat notes that it will begin, and Kosh agrees.

On Earth, Commander John Sheridan is brought to Lefcourt for the mission to Minbari space as first officer on the EAS Prometheus. Sheridan does not like it, as its captain, Michael Jankowski, had trouble with a first contact situation before, and he feels like he needs to continue serving his current captain, Roger Sterns. Lefcourt insists this is not a good career move and that Jankowski was cleared, but Sheridan refuses.

In hyperspace, Delenn notes an unusually risky cargo transport to the ship and confronts the pilot. He does not know much, only that it i life support equipment and he acted under Dukhat's orders. Dukhat himself comes around the corner, politely challenging her for looking into details. Delenn tries to get him to admit there is a Vorlon on board, but he does not let on.

The Prometheus comes out of hyperspace and its XO finds the silhouettes of the Minbari ships outside Minbari space. Despite his objections that they have are to avoid first contact, Jankowski is determined to get the information they came for and orders the ship closer.

Meanwhile, Delenn is undergoing a ritual to formally become part of the Grey Council. Dukhat leads her alone into the Council chamber and holds a triluminary to her, glowing and surprising the other Council member nearby. After the ritual, Morann tells the other members that they detected the human ships, but will not inform Dukhat until they know more. They change course toward them, which prompts Jankowski to take his ship out, but they cannot start their jump engines. Dukhat is finally informed and shocked at the presence of the aliens, and that their gun ports are open. The EA XO cannot tell whether the Minbari ships are hostile, only that their gun ports are open. Soon, though, he then believes they are locking on and Jankowski orders the ship to fire. The Minbari ship is taken by surprise and Dukhat is mortally wounded. He speaks to Delenn and then collapses. The Council is divided about retaliating, and a furious Delenn casts the deciding vote – The Minbari will go to war with the Humans.

Mollari describes the Minbari's domination at beginning of the holy war.

General Lefcourt addresses a large crowd of EA officers on their losing situation aside General Fontaine. The Minbari are systematically destroying military targets and leaving civilian ones alone, presumably saving them for later since they have a warrior caste. Fontaine believes they are dedicated to wiping all Humans out, and notes their stealth technology is still a huge advantage. They need any victory at all. As the crowd dismisses, Sheridan and Sterns talk. Sheridan believes any ship can be beat. Sterns recommends Sheridan visit his family while the Lexington is fully outfitted, but Sheridan wants to stay.

In a fighter bay, Ganya Ivanov gets a visit from his sister, Susan. She is very worried about him, but Ganya is very confident. She tells him she has decided to sign up for Earthforce, which worries him as their father will not allow it. Susan expected the reaction, but she's determined. She makes Ganya take one of her earrings as good luck, expecting him to return it to her when he makes it back.

Mollari is approached by Hastur and asked for strategic support and weapons. Mollari refuses, not wanting to incur retaliation on the Centauri Republic. Hastur then goes into an office and meets G'Kar, who had predicted Mollari's response. He is happy to make the deal, as the Narn have captured and studied Centauri weapons and doesn't fear retaliation since the Minbari will assume it was the Centauri. G'Kar negotiates a higher price due to the falling Earth currency.

Morann meets Lenonn and Delenn to inform them of the falling of three more deep-range Human colonies. Delenn is not responsive, and Morann challenges her lack of enthusiasm. She notes the Humans do not have a chance, and it has gone beyond retribution at this point. Lenonn chimes in, wondering why the warrior caste is so enthusiastic about the War. Morann says they're a tangible enemy, unlike what the Anla'Shok have been saying for centuries. Lenonn, however, notes it is an easy war and an easy victory for them. Morann challenges Lenonn's loyalty, which prompts Delenn to demand he leave at once. After he goes, Lenonn apologizes for the exchange and suggests she go to Dukhat's private chamber as soon as she can.

There, Delenn is shocked to find Kosh and Ulkesh (though they do not introduce themselves). She timidly asks if they are Vorlon and asks their name, to which only Kosh responds with his name. Delenn is shown a posthumous message of Dukhat, revealing his knowledge of the Vorlons' presence, their intention to help them, and that they must find the Humans and make them allies. He knew the Shadows were gathering and he insists whoever views his message finish what he started. Then, Lenonn appears, declaring they must stop the War.

Stephen Franklin is introducing a number of officers to a new medical facility when General Fontaine interrupts, clearly angered by something. Franklin dismisses the group and Fontaine reveals he has been informed of Franklin's activities, particularly his knowledge of Minbari anatomy and DNA. Angry he has not provided this information to Earthforce, he demands Franklin's notes, but he refuses, as his commitment to being a doctor prohibits him from helping to develop bio-engineered weapons. Fontaine has him arrested and all his property searched for the medical data.

On the Lexington, Sheridan records a log, saying they have lost two more ships, probably to soften them for another attack. Stern has not slept in two days, and there is a rumor of an ace ship destroying a lot of ships. Then, Sheridan confirms a Minbari short-range ship, probably a scout or straggler. Stern doesn't want to pursue, but instead orders a single fighter to investigate. Ivanov is the one chosen, and he follows the ship through an asteroid field only to see it stop as if the pilot died. Sheridan notes its forward thruster fired, suggesting it meant to stop. As they argue, they realize it is a trap. The ship quickly becomes active and destroys Ivanov's starfury as a Minbari cruiser jumps in and attacks. Sheridan turns around to see Stern has died.

Delenn has to find out how to stop the War. She proposes to Lenonn that they need to open negotiations through someone unofficial but also respected. She suggests he go and use the Narn as a contact under the guise of making a weapons deal. He agrees, seeing a real chance at helping their people even though it is dangerous.

The Lexington is dead in space, grazed by a few odd asteroids. Sheridan pauses and comes up with a plan: plant a few nuclear bombs in the asteroid field and send a distress signal, probably drawing the Minbari ship back which had figured them for dead. He looks to the others for disagreement, and no one speaks.

The Lexington crew finishes placing the bombs, and Sheridan orders the signal. Soon, communications verifies the arrival of the ship. Sheridan orders the ship to move as if it is evading. He puts a picture on his panel, then gives the order to trigger the bombs. Two explosions later, the ship is destroyed.

Later, an EA crowd cheers at the news of Sheridan's maneuver. General Lefcourt explains the ship was the Black Star, one of their greatest ships. He reminds the crowd that the Minbari do not take prisoners and any questions of morality about the maneuver should be answered with that. He dismisses the crowd and takes Sheridan aside for a mission. Sheridan meets G'Kar and is explained that there is a Minbari faction that wants to rendezvous and negotiate an end to the War. He is to evaluate the truthfulness of the claim with G'Kar to translate if needed. Franklin is brought in to be part of the mission, able to verify the contact. Provided the claim is verified, negotiators will come in later.

Back in the Centauri palace, Mollari notes everyone has their orders, including the children. The Centauri had heard of the EA-Minbari rendezvous and assumed it was an arms deal, not a mission to end the war. He himself ordered a Centauri ship to intercept.

Sheridan, Franklin, and G'Kar arrive at the listening post. Franklin goes to check the perimeter, and comes back with Lenonn holding him at gunpoint. In broken English, he presumes Sheridan's name. He says he knows a lot about them, including the Black Star. He declares they must stop the war, but then G'Kar gets a message about an incoming ship, but not who it is. The Centauri ship quickly destroys the Narn transport and fires on the planet. Lenonn is critically hurt, but with no way to get help the other three can only take the debris off of him. Lenonn says disappointingly he believes the Minbari will take this as an attack. He takes Sheridan close and whispers something to him before he dies.

Indeed, the three are quickly taken to a Minbari cruiser. Sheridan and Franklin are told they will be executed, but then Sheridan yells that he knows what is in Dukhat's sacred place. Delenn is there, hooded, and turns around, asking for explanation. Sheridan declares it is isil'zha – the future. Delenn, without revealing herself, takes a pause and realizes what happened to Lenonn. She has them let go.

Emperor Mollari says the War continued to escalate even after 50 or 60 thousand died.

Mollari explains he was afraid of what was happening outside the palace, and decided to have the windows barred. Despite having four wives he loved greatly, he loved Centauri Prime above all. It's on fire, now. There is hope, but it will be hard. He turns back to the story.

The Humans knew they were doomed, but fought back anyway, making the Minbari fight for every inch over two years.

In a fighter bay, the President informs everyone that the mid-range bases at Beta Durani I and Proxima III have fallen, and contact with Io has been lost. The EA believes the Minbari will skip Mars and hit Earth. They've broadcast their surrender, but with no response. She asks for every ship possible to get together the last defense of Earth to buy time for transports to evacuate to neutral territory.

With hundreds of ships gathered for the Battle of the Line, Delenn waits. Coplann comes to bring her to see the battle, and she wonders if it's holy anymore. He can't answer, and asks her to bring her questions to the Council.

Delenn first goes to Dukhat's room and asks for Kosh. He appears and responds cryptically that he has always been there. She declares she has failed. Even Morann is tired of war, but it has a life of its own now that can't be stopped. She believes they only need a simple reason to delay, but doesn't know what to do. They don't respond, but as she leaves, Kosh suggests "the truth points to itself." She doesn't understand, and Ulkesh responds simply, "you will understand." They send her away.

An EA scout investigates a signal, only to find a scouting party that kills him. The battle begins. Jeffrey Sinclair is there with Bill Mitchell, who is killed in a trap. As the fight starts, Delenn notes they're brave, while Coplann notes it could just be desperation. Delenn decides she wants to bring a Human aboard for questioning, and, as Sinclair has decided to ram the Minbari cruiser, she chooses him. Coplann arranges for the interrogation.

After the interrogation ends, Coplann has found something shocking and hurriedly goes to Delenn. He says she and the rest of the Council needs to see what he found.

Sinclair, strapped to a hanging bar, is tested again by a hooded Minbari (Delenn) by a triluminary. It glows. She goes to the rest of the Council and it's confirmed: He has a Minbari soul – Valen's, in fact. Delenn deduces he must have been reborn in a Human in order to indicate that this race would be important to them. The Council now can order the war stopped, and Morann notes Sinclair must not remember his encounter. Delenn calls for some telepaths.

In 2278, Mollari describes the mystery surrounding the end of the War, and that's the end of the story.

The President of Earth broadcasts the Babylon Project and its mission. The first station, Babylon 1, was destroyed, but it would just take time.

Senna puts the seal back on Mollari, and he thanks her for having the children here, as it made him laugh. Luc promises to remember the story. As they go, he says Sheridan became the president of a great alliance and that Delenn was at his side. After the children go, he orders more alcohol and sends for the prisoners. He opens a camera into the cell, revealing Sheridan and Delenn themselves are in the cell.

The film raises a few questions that at first glance appear to contradict the established version of events.

Of particular note are the details surrounding the destruction of the Black Star. Specifically, in "Points of Departure," Sheridan states the following: "I hit on the idea of mining the asteroid field between Jupiter and Mars. A fusion bomb doesn't have to lock on to anything if it's close enough. It took out the Black Star and three heavy cruisers before they could escape."

While no information is given within the movie as to the timing and location of the battle, the Black Star appears to be alone and the three heavy cruisers Sheridan mentions are nowhere to be seen. The only clue to the timing of the event comes, again, from "Points of Departure", when Sheridan mentions that it has been twelve years (from early 2259) since the incident. This places it in 2247, which is consistent with Ivanova's age at the time (see below.)

Ivanova's age is sometimes brought up as being inconsistent, but this is incorrect. Her birth year is established in "Eyes" as 2230, while "Sic Transit Vir" establishes that she enlisted in 2247, making her sixteen (a few months short of seventeen) during the scene between her and Ganya Ivanov.

Confusion surrounding Ivanova's age comes from the episodes "TKO" and "The Long Night". In "TKO", Rabbi Koslov states that the death of Susan's mother was a year prior to Ganya's, placing Susan in her early to mid teens, as above, while Susan's own account of the incident in "The Long Night" leaves one with the impression that she was just a small child at the time.

The scene that featured a brief confrontation between Lenonn and Morann in Delenn's quarters was trimmed down from what was originally scripted and shot. The exchange was originally much more heated and culminated in Lenonn drawing his pike on Morann before Delenn can get between them and order Morann out.

This was the second and final time after season 1 that Mira Furlan filmed flashback scenes in her original full Minbari makeup (the other being the season 4 episode "Atonement").